Tag: kegg
Microbially produced vitamin B12 contributes to the lipid-lowering effect of silymarin
Animals As female mice/rats resist to HFD-induced obesity and NAFLD, male mice/rats were used to induce obesity and NAFLD model by HFD50. Male Wistar (~180 g body weight; 8 weeks old) rats were purchased from Shandong Laboratory Animal Center with the permission number of SCXK 2014–0007 and raised under thermoneutral housing…
Screening of lymphoma radiotherapy-resistant genes
Introduction Lymphoma, a cancer characterized by a malignant tumor of the immune system that originates in the lymph nodes or lymphoid tissue, is one of the most common cancers worldwide. According to GLOBOCAN, the incidence of non-Hodgkin lymphoma (NHL) in both males and females ranked top ten among all cancers…
Virulence and antibiotic-resistance genes in Enterococcus faecalis associated with streptococcosis disease in fish
Isolation, phenotypic identification, pathogenicity and antibiogram profiling Enterococcus faecalis strains BFF1B1, BFFF11 and BFPS6 were cultured in Streptococcus selective agar media (Himedia, India). The culture characteristics such as colony, morphological, physiological and biochemical characteristics of these strains BFF1B1, BFFF11 and BFPS6 were summarized in the Supplementary Table S1. All of…
Recommendations needed for a tool for comparative gene set enrichment analyses via a webserver
Recommendations needed for a tool for comparative gene set enrichment analyses via a webserver 1 dear All, I’d like to compare 6 gene expression datasets (multiple conditions / time-points) in terms of joint patterns in the enrichments of the differentially expressed genes. The DEG lists I have prepared (logFC,padj). GO…
Maternal diet induces persistent DNA methylation changes in the muscle of beef calves
Gicquel, C., El-Osta, A. & Le Bouc, Y. Epigenetic regulation and fetal programming. Best Pract. Res. Clin. Endocrinol. Metab. 22, 1–16 (2008). CAS Google Scholar Godfrey, K. M. & Barker, D. J. Fetal programming and adult health. Public Health Nutr. 4, 611–624 (2001). CAS Google Scholar Encinias, H. B., Lardy,…
Scientist II, Bioinformatics Job Opening in South Plainfield, NJ at PTC Therapeutics, Inc.
Job Posting for Scientist II, Bioinformatics at PTC Therapeutics, Inc. Job Description Summary: The Scientist II, Bioinformatics is responsible for planning and performing scientific experiments that contribute to PTC’s research and drug discovery activities. The Scientist II is also responsible for communicating experimental results to his/her supervisor and…
cluster profiler for pathway analysis in scRNA Seq
Dear Community, I am trying to show pathway expression in 6 clusters that I identified in disease and control and would like to compare the corresponding clusters. I followed this post 438466 and used Pratik ‘s solution. Which gives me a plot only for the disease. However, I would like…
Annelid functional genomics reveal the origins of bilaterian life cycles
Hall, B. K. & Wake, M. H. in The Origin and Evolution of Larval Forms (eds Hall, B. K. & Wake, M. H.) 1–19 (Academic Press, 1999). Nielsen, C. Animal phylogeny in the light of the trochaea theory. Biol. J. Linn. Soc. 25, 243–299 (2008). Article Google Scholar Garstang, W….
Closed genomes uncover a saltwater species of Candidatus Electronema and shed new light on the boundary between marine and freshwater cable bacteria
Pfeffer C, Larsen S, Song J, Dong M, Besenbacher F, Meyer RL, et al. Filamentous bacteria transport electrons over centimetre distances. Nature. 2012;491:218–21. Article CAS Google Scholar Lovley DR, Holmes DE. Electromicrobiology: the ecophysiology of phylogenetically diverse electroactive microorganisms. Nat Rev Microbiol. 2022;20:5–19. Article CAS Google Scholar Bjerg JT, Boschker…
single pathway score
single pathway score 1 Hello, I would like to find out a method for “single pathway” differential analysis (if it exists). For example, our team is focused in KEGG pathway hsa03018 (RNA degradation). Our transcriptome data (Treatment vs Control) underwent differential analysis as usual, and GSEA: I happily obtained a…
Harshening stem cell research and precision medicine: The states of human pluripotent cells stem cell repository diversity, and racial and sex differences in transcriptomes
doi: 10.3389/fcell.2022.1071243. eCollection 2022. Affiliations Expand Affiliations 1 Department of Anatomy, Biochemistry and Physiology, Honolulu, HI, United States. 2 Center for Cardiovascular Research, Honolulu, HI, United States. 3 Department of Medicine, Honolulu, HI, United States. 4 Department of Quantitative Health Sciences, Honolulu, HI, United States. 5 Genomics and Bioinformatics Shared…
Genomic analysis of an ultrasmall freshwater green alga, Medakamo hakoo
Materials Medakamo hakoo 311 was obtained from the personal aquarium of Prof. Kuroiwa (Kagurazaka, Tokyo, Japan)4. The M. hakoo strain was cultured in 0.05% HYPONeX (HYPONeX Japan Corp., Ltd., Osaka, Japan) liquid medium and on 0.05% HYPONeX gellan gum-based solid medium in plates. Cyanidioschyzon merolae 10D (Toda et al. 1995)…
KEGG T01001: 5742
Entry 5743 CDS T01001 Symbol PTGS2, COX-2, COX2, GRIPGHS, PGG/HS, PGHS-2, PHS-2, hCox-2 Name (RefSeq) prostaglandin-endoperoxide synthase 2 KO K11987 prostaglandin-endoperoxide synthase 2 [EC:1.14.99.1] Organism hsa Homo sapiens (human) Pathway hsa00590 Arachidonic acid metabolism hsa01100 Metabolic pathways hsa04064 NF-kappa B signaling pathway hsa04370 VEGF signaling pathway hsa04625 C-type lectin receptor signaling pathway hsa04657 …
Transcriptome and 16S rRNA Analyses Reveal That Hypoxic Stress Affects the Antioxidant Capacity of Largemouth Bass ( Micropterus salmoides), Resulting in Intestinal Tissue Damage and Structural Changes in Microflora
doi: 10.3390/antiox12010001. Affiliations Expand Affiliations 1 Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China. 2 Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China. Free PMC article Item in Clipboard Zhuo…
Identification of genetic variants associated with diabetic kidney disease in multiple Korean cohorts via a genome-wide association study mega-analysis | BMC Medicine
Tuttle KR, Bakris GL, Bilous RW, Chiang JL, de Boer IH, Goldstein-Fuchs J, et al. Diabetic kidney disease: a report from an ADA Consensus Conference. Diabetes Care. 2014;37(10):2864–83. Article Google Scholar Jha V, Garcia-Garcia G, Iseki K, Li Z, Naicker S, Plattner B, et al. Chronic kidney disease: global dimension…
Hypersaline Lake Urmia: a potential hotspot for microbial genomic variation
Physico-chemical features of Lake Urmia Sampling was performed during the period of lowest rainfall and input volume in the year when the lake water reached the highest salt concentration (locations shown in Fig. 1, Supplementary Table S1). The measured ionic composition of the collected brine showed the typical composition of halite-dominated…
KEGG COMPOUND: C01588
KEGG COMPOUND: C01588 COMPOUND: C01588 Help Entry C01588 Compound Name Formula C13H18O2 Exact mass 206.1307 Mol weight 206.2808 Structure Mol fileKCF fileDB search Remark Brite Anatomical Therapeutic Chemical (ATC) classification [BR:br08303] C CARDIOVASCULAR SYSTEM C01 CARDIAC THERAPY C01E OTHER CARDIAC PREPARATIONS C01EB Other cardiac preparations C01EB16 Ibuprofen D00126 Ibuprofen (JP18/USP/INN) <JP/US> G GENITO URINARY SYSTEM AND SEX HORMONES G02…
KEGG COMPOUND: C03323
KEGG COMPOUND: C03323 COMPOUND: C03323 Help Entry C03323 Compound Name (2,1-beta-D-Fructosyl)n;(2,1-beta-D-Fructosyl)n+1;Inulin;(1,2-beta-D-Fructosyl)n;(1,2-beta-D-Fructosyl)m;(1,2-beta-D-Fructosyl)n+1;(1,2-beta-D-Fructosyl)m-1 Formula (C12H20O10)n Structure Mol fileKCF fileDB search Remark Reaction Pathway map00500 Starch and sucrose metabolism Enzyme Brite Therapeutic category of drugs in Japan [BR:br08301] 7 Agents not mainly for therapeutic purpose 72 Intracorporeal diagnostic agents 722 Various function testing reagents 7225 Diagnostic reagents for renal function D00171 Inulin (JAN/USP)New…
Unexpected absence of ribosomal protein genes from metagenome-assembled genomes
Hug LA, Baker BJ, Anantharaman K, Brown CT, Probst AJ, Castelle CJ, et al. A new view of the tree of life. Nat Microbiol. 2016;1:16048. Article PubMed Google Scholar Castelle CJ, Wrighton KC, Thomas BC, Hug LA, Brown CT, Wilkins MJ, et al. Genomic expansion of domain archaea highlights roles…
Community succession and functional prediction of microbial consortium with straw degradation during subculture at low temperature
Changes of straw degradation characteristics at different culture stages Corn straw degradation ratio Corn straw weight loss in M44 at F1 reached 35.90% at 15 ℃ for 21 days, which was greater than that at F5, F8, and F11 by 2.33%, 3.01%, and 3.35%, respectively. There were no significant differences between…
KEGG ORTHOLOGY: K16408
KEGG ORTHOLOGY: K16408 ORTHOLOGY: K16408 Help Entry K16408 Tight KO Symbol stiD Name stigmatellin polyketide synthase StiD Pathway map01052 Type I polyketide structures Brite KEGG Orthology (KO) [BR:ko00001] 09100 Metabolism 09109 Metabolism of terpenoids and polyketides 01052 Type I polyketide structures K16408 stiD; stigmatellin polyketide synthase StiD 09180 Brite Hierarchies 09181 Protein families: metabolism 01008 Polyketide biosynthesis proteins K16408 stiD; stigmatellin…
Assessing spermatozoal small ribonucleic acids and their relationship to blastocyst development in idiopathic infertile males
Vander, B. M. & Wyns, C. Fertility and infertility: Definition and epidemiology. Clin. Biochem. 62, (2018). Sun, H. et al. Global, regional, and national prevalence and disability-adjusted life-years for infertility in 195 countries and territories, 1990–2017: Results from a global burden of disease study, 2017. Aging 11, 10952 (2019). Article …
Plasma metabolomics and gene regulatory networks analysis reveal the role of nonstructural SARS-CoV-2 viral proteins in metabolic dysregulation in COVID-19 patients
The metabolite content in plasma samples of COVID-19 patient and control cohorts is shown in the Supplementary Data. The filtration of metabolites was first approached. Only those metabolites that showed the non-zero values in at least two of three repeats were used for the further analysis. Thus, only 140 metabolites…
KEGG ENZYME: 1.16.1.1
KEGG ENZYME: 1.16.1.1 ENZYME: 1.16.1.1 Help Entry EC 1.16.1.1 Enzyme Name mercury(II) reductase;mercuric reductase;mercurate(II) reductase;mercuric ion reductase;mercury reductase;reduced NADP:mercuric ion oxidoreductase;mer A Class Oxidoreductases;Oxidizing metal ions;With NAD+ or NADP+ as acceptorBRITE hierarchy Sysname Hg:NADP+ oxidoreductase Reaction(IUBMB) Hg + NADP+ + H+ = Hg2+ + NADPH [RN:R02807] Reaction(KEGG) Substrate Product Comment A…
Obtaining directionality of pathways
Obtaining directionality of pathways 0 I am attempting to use R to extract biological pathway information from several different online databases (specifically KEGG, Wikipathways and Reactome) and use that information in a larger project I am working on where I am attempting to gauge levels of pathway functionality. An important…
Exploring structure, microbiota, and metagenome functions of epigean and hypogean black deposits by microscopic, molecular and bioinformatic approaches
Spiro, T. G., Bargar, J. R., Sposito, G. & Tebo, B. M. Bacteriogenic manganese oxides. Acc. Chem. Res. 43, 2–9. doi.org/10.1021/ar800232a (2010). Article CAS PubMed Google Scholar Roitz, J. S., Flegal, A. R. & Bruland, K. W. The biogeochemical cycling of manganese in San Francisco Bay: Temporal and spatial variations…
What is Kegg orthology and what is it used for? : bioinformatics
Kegg orthology is a database of genes with known identity and function. You can submit genomic data to be referenced against that database. I love using kegg to produce genome summaries such as what metabolic pathways are complete and incomplete, and what percentage of genes in the genome are dedicated…
KEGG T00005: YNL036W
Entry YNL036W CDS T00005 Symbol NCE103, NCE3 Name (RefSeq) carbonate dehydratase NCE103 KO K01673 carbonic anhydrase [EC:4.2.1.1] Organism sce Saccharomyces cerevisiae (budding yeast) Pathway sce00910 Nitrogen metabolism sce01100 Metabolic pathways Brite KEGG Orthology (KO) [BR:sce00001] 09100 Metabolism 09102 Energy metabolism 00910 Nitrogen metabolism YNL036W (NCE103)Enzymes [BR:sce01000] 4. Lyases 4.2 Carbon-oxygen lyases 4.2.1 Hydro-lyases 4.2.1.1 carbonic anhydrase YNL036W (NCE103) BRITE hierarchy SSDB OrthologParalogGene clusterGFIT Motif Pfam: …
Dual roles of mTORC1-dependent activation of the ubiquitin-proteasome system in muscle proteostasis
Sustained skeletal muscle mTORC1 activity upregulates the ubiquitin proteasome system To understand the molecular mechanisms causing atrophy in muscles with high mTORC1 activation, we first analyzed the transcriptome of the fast-type extensor digitorum longus (EDL) muscle in 3-month-old TSCmKO mice6. A short-term (3 day) treatment with rapamycin was used to…
Comprehensive Analysis of NPSR1-AS1 as a Novel Diagnostic and Prognostic Biomarker Involved in Immune Infiltrates in Lung Adenocarcinoma
The incidence of lung adenocarcinoma (LUAD), the most common subtype of lung cancer, continues to make lung cancer the largest cause of cancer-related deaths worldwide. Long noncoding RNAs (lncRNAs) have been shown to have a significant role in both the onset and progression of lung cancer. In this study, we…
GWAS, MWAS and mGWAS provide insights into precision agriculture based on genotype-dependent microbial effects in foxtail millet
GWAS identifies genetic variations associated with agronomic traits in foxtail millet A total of 827 foxtail millet cultivars collected from China were sequenced and genotyped using common single-nucleotide polymorphisms (SNPs) based on a ~423 Mb Setaria italica cv. Zhanggu reference genome (v.2.3)27. In total, 161,562 SNPs were detected after stringent steps…
Job – Principal Biostistician/Bioinformatics job at Kenya Medical Research
Vacancy title: Principal Biostistician/Bioinformatics [ Type: FULL TIME , Industry: Research , Category: Research ] Jobs at: Kenya Medical Research – KEMRI Deadline of this Job: 06 October 2022 Duty Station: Within Kenya , Kisumu , East Africa SummaryDate Posted: Tuesday, September 20, 2022 , Base Salary: Not Disclosed…
KEGG COMPOUND: C00236
KEGG COMPOUND: C00236 COMPOUND: C00236 Help Entry C00236 Compound Name 3-Phospho-D-glyceroyl phosphate;1,3-Bisphospho-D-glycerate;(R)-2-Hydroxy-3-(phosphonooxy)-1-monoanhydride with phosphoric propanoic acid;D-Glycerate 1,3-diphosphate Formula C3H8O10P2 Exact mass 265.9593 Mol weight 266.0371 Structure Mol fileKCF fileDB search Reaction Pathway map00010 Glycolysis / Gluconeogenesis map00710 Carbon fixation in photosynthetic organisms map01060 Biosynthesis of plant secondary metabolites map01061 Biosynthesis…
KEGG ORTHOLOGY: K17753
KEGG ORTHOLOGY: K17753 ORTHOLOGY: K17753 Help Entry K17753 KO Symbol HICDH Name isocitrate–homoisocitrate dehydrogenase [EC:1.1.1.286] Pathway map01110 Biosynthesis of secondary metabolites map01120 Microbial metabolism in diverse environments map01210 2-Oxocarboxylic acid metabolism Brite KEGG Orthology (KO) [BR:ko00001] 09100 Metabolism 09101 Carbohydrate metabolism 00020 Citrate cycle (TCA cycle) K17753 HICDH; isocitrate–homoisocitrate dehydrogenase 09105 Amino acid metabolism 00300 Lysine biosynthesis K17753 HICDH;…
KEGG COMPOUND: C00509
KEGG COMPOUND: C00509 COMPOUND: C00509 Help Entry C00509 Compound Name Naringenin;4′,5,7-Trihydroxyflavanone;(2S)-Naringenin;(-)-(2S)-Naringenin Formula C15H12O5 Exact mass 272.0685 Mol weight 272.2528 Structure Mol fileKCF fileDB search Reaction Pathway map01061 Biosynthesis of phenylpropanoids map01110 Biosynthesis of secondary metabolites Module M00137 Flavanone biosynthesis, phenylalanine => naringenin M00138 Flavonoid biosynthesis, naringenin => pelargonidin M00941 Isoflavone…
Data Scientist – Bioinformatics at Faculty – London, England, United Kingdom
Faculty is one of Europe’s leading applied artificial intelligence companies. We build, deploy and operate AI solutions to increase our customers’ performance and help them realise their full potential. We believe that AI should be trustworthy, impactful and beneficial across society. Those principles have shaped our work with more than…
KEGG T01001: 4171
Entry 4171 CDS T01001 Symbol MCM2, BM28, CCNL1, CDCL1, D3S3194, DFNA70, MITOTIN, cdc19 Name (RefSeq) minichromosome maintenance complex component 2 KO K02540 DNA replication licensing factor MCM2 [EC:5.6.2.3] Organism hsa Homo sapiens (human) Pathway hsa03030 DNA replication hsa04110 Cell cycle Disease H00604 Deafness, autosomal dominant Brite KEGG Orthology (KO) [BR:hsa00001] 09120 Genetic Information Processing 09124…
KEGG T02666: 101290786
Entry 101298727 CDS T02666 Name (RefSeq) triacylglycerol lipase SDP1 KO K14674 TAG lipase / steryl ester hydrolase / phospholipase A2 / LPA acyltransferase [EC:3.1.1.3 3.1.1.13 3.1.1.4 2.3.1.51] Organism fve Fragaria vesca (woodland strawberry) Pathway fve00100 Steroid biosynthesis fve00561 Glycerolipid metabolism fve00564 Glycerophospholipid metabolism fve00565 Ether lipid metabolism fve00590 Arachidonic acid metabolism fve00591 Linoleic…
Bioinformatics Analysis of the Key Genes and Pathways in Multiple Myel
Introduction Multiple myeloma is a B-cell malignancy characterized by the malignant proliferation of clonal plasma cells in bone marrow,1 It is the second most common hematological malignancy after lymphoma.2 The age-standardised rate (ASR) of multiple myeloma incidence was 1·78 (95% UI 1·69-1·87) per 100 000 people globally and mortality was…
KEGG COMPOUND: C03793
KEGG COMPOUND: C03793 COMPOUND: C03793 Help Entry C03793 Compound Name N6,N6,N6-Trimethyl-L-lysine Formula C9H20N2O2 Exact mass 188.1525 Mol weight 188.2673 Structure Mol fileKCF fileDB search Reaction Pathway Enzyme Other DBs KCF data Show ATOM 13 1 N1d N 30.1000 -20.2300 #+ 2 C1b C 28.9100 -20.9300 3 C1a C 31.2900 -20.9300 4 C1a C 30.1000 -18.8300 5 C1a C 29.8200 -21.8400 6 C1b C 27.6500 -20.2300 7 C1b C 26.4600 -20.9300 8 C1b C 25.2700 -20.2300 9 C1c C 24.0100 -20.9300 10 C6a C 22.8200 -20.2300 11 N1a N 24.0100 -22.3300 12 O6a O 22.8200 -18.8300 13 O6a O 21.4900 -20.8600 #-BOND 12 1 1 2 1 2 1 3 1 3 1 4…
KEGG COMPOUND: C17729
KEGG COMPOUND: C17729 COMPOUND: C17729 Help Entry C17729 Compound Name Nicofetamide;N-(1,2-Diphenylethyl)nicotinamide Formula C20H18N2O Exact mass 302.1419 Mol weight 302.3697 Structure Mol fileKCF fileDB search Remark Brite Anatomical Therapeutic Chemical (ATC) classification [BR:br08303] A ALIMENTARY TRACT AND METABOLISM A03 DRUGS FOR FUNCTIONAL GASTROINTESTINAL DISORDERS A03A DRUGS FOR FUNCTIONAL GASTROINTESTINAL DISORDERS A03AC Synthetic antispasmodics, amides with…
Differential enrichment of H3K9me3 in intrahepatic cholangiocarcinoma | BMC Medical Genomics
Sia D, Tovar V, Moeini A, Llovet JM. Intrahepatic cholangiocarcinoma: pathogenesis and rationale for molecular therapies. Oncogene. 2013;32(41):4861–70. CAS Article Google Scholar Sungwan P, Lert-Itthiporn W, Silsirivanit A, Klinhom-On N, Okada S, Wongkham S, Seubwai W. Bioinformatics analysis identified CDC20 as a potential drug target for cholangiocarcinoma. PeerJ. 2021;9:e11067. Article …
Acute phase of ischemia-reperfusion in rats
Introduction Stroke is one of the leading causes of death and disability worldwide, which causes substantial economic and social burdens.1 Ischemic stroke is caused by insufficient blood and oxygen supply to the brain,2 accounting for about 85% of the casualties of stroke patients.3 The concept of treatment for ischemic injury…
CRISPRa screen identifies a role for c-KIT signaling in tamoxifen resistance, potentially through upregulation of ABC transporters
Abstract Resistance to endocrine therapy is a common problem in patients with estrogen receptor alpha (ERα) positive breast cancer. In this study, we took a non-biased genome-wide approach to identify novel mechanisms of endocrine resistance using a clustered regularly interspaced short palindromic repeats (CRISPR) activating (CRISPRa) screen. Results from the…
uniprot – How to annotate list of proteins with KEGG orthology groups?
I’ve got a list of proteins, complete with Uniprot IDs. I’d like to group them into orthology groups based on data from KEGG, but I have no idea how to add a column with KEGG groups. I’ve tried poking around in the documentation for UniProt, but all I can find…
KEGG REACTION: R11822
KEGG REACTION: R11822 REACTION: R11822 Help Entry R11822 Reaction Name (2E,6E)-farnesyl-diphosphate diphosphate-lyase [cyclizing, (+)-isoafricanol-forming] Definition trans,trans-Farnesyl diphosphate + H2O <=> (+)-Isoafricanol + Diphosphate Equation Enzyme Other DBs LinkDB All DBs DBGET integrated database retrieval system Read more here: Source link
Transcription-independent regulation of STING activation and innate immune responses by IRF8 in monocytes
Reagents, antibodies, viruses and cells LMW-Poly(I:C), LPS, 2′3′-cGAMP and DMXAA (InvivoGen); hydroxyurea, camptothecin and mitomycin C (MCE); GM-CSF, Flt3L (peproTech); lipofectamine 2000 (Invitrogen); polybrene (Millipore); RNAiso Plus (Takara); HT-DNA (Sigma); SYBR (BIO-RAD); dual-specific luciferase assay kit (Promega); ELISA kit for murine Ifn-β (PBL); ELISA kits for murine IP-10 (Biolegend) were…
KEGG ENZYME: 6.2.1.11
KEGG ENZYME: 6.2.1.11 ENZYME: 6.2.1.11 Help Entry EC 6.2.1.11 Enzyme Name biotin—CoA ligase;biotinyl-CoA synthetase;biotin CoA synthetase;biotinyl coenzyme A synthetase Class Ligases;Forming carbon-sulfur bonds;Acid-thiol ligasesBRITE hierarchy Sysname biotin:CoA ligase (AMP-forming) Reaction(IUBMB) ATP + biotin + CoA = AMP + diphosphate + biotinyl-CoA [RN:R01075] Reaction(KEGG) Substrate Product History EC 6.2.1.11 created 1972 Pathway…
In vivo transomic analyses of glucose-responsive metabolism in skeletal muscle reveal core differences between the healthy and obese states
Animals and sample preparation Animal experiments were performed as previously described12. C57BL/6J WT mice or ob/ob mice at ten weeks of age were purchased from Japan SLC Inc. (Shizuoka, Japan). The phenotypic data of the mice are summarized in Table S1. Animal experiments were approved by the animal ethics committee…
KEGG ENZYME: 3.6.1.39
KEGG ENZYME: 3.6.1.39 ENZYME: 3.6.1.39 Help Entry EC 3.6.1.39 Enzyme Name thymidine-triphosphatase;thymidine triphosphate nucleotidohydrolase;dTTPase;deoxythymidine-5′-triphosphatase Class Hydrolases;Acting on acid anhydrides;In phosphorus-containing anhydridesBRITE hierarchy Sysname dTTP nucleotidohydrolase Reaction(IUBMB) dTTP + H2O = dTDP + phosphate [RN:R02095] Reaction(KEGG) Substrate Product Comment Also acts, more slowly, on dUTP and UTP. History EC 3.6.1.39 created 1984…
KEGG REACTION: R00134
Entry R00134 Reaction Name formate:NADP+ oxidoreductase Definition Formate + NADP+ <=> CO2 + NADPH + H+ Equation Reaction class Enzyme Pathway rn00720 Carbon fixation pathways in prokaryotes rn01120 Microbial metabolism in diverse environments Module M00377 Reductive acetyl-CoA pathway (Wood-Ljungdahl pathway) Orthology Other DBs LinkDB All DBs Read more here: Source link
KEGG T01015: 107278078
Entry 4330855 CDS T01015 Name (RefSeq) auxin-responsive protein SAUR32 KO K14488 SAUR family protein Organism osa Oryza sativa japonica (Japanese rice) (RefSeq) Pathway osa04075 Plant hormone signal transduction Brite KEGG Orthology (KO) [BR:osa00001] 09130 Environmental Information Processing 09132 Signal transduction 04075 Plant hormone signal transduction 4330855 BRITE hierarchy SSDB OrthologParalogGene clusterGFIT Motif Pfam: Auxin_inducible Motif Other DBs…
Dietary selection of metabolically distinct microorganisms drives hydrogen metabolism in ruminants
Volatile fatty acid production and absorption is modulated by diet Animals were adapted to a starch-rich diet by gradually increasing dietary concentrate content from 50 to 90% over the three 100-d experimental periods (Fig. 1A). With both diets, rumen structure and epithelial morphology were robust and rumen pH remained above 6.0…
Targeted inhibition of ubiquitin signaling reverses metabolic reprogramming and suppresses glioblastoma growth
Cell culture Human glioblastoma cells (U87MG and U87MG-Luc) and human embryonic kidney cells (HEK293) were obtained from the American Type Culture Collection (Manassas, Va.). Cells were cultured in Dulbecco’s Modified Eagle Medium supplemented with 10% fetal bovine serum (Gibco™ Fetal Bovine Serum South America, Thermo Scientific Fisher-US), 2 mM l-glutamine, 50 U/ml…
Genomic architecture of adaptive radiation and hybridization in Alpine whitefish
Sampling the radiation To understand the phylogenetic relationships between Alpine whitefish, we carried out whole-genome resequencing on 96 previously collected whitefish (with associated phenotypic measurements including standard length and gill-raker counts; collected in accordance with permits issued by the cantons of Zurich (ZH128/15), Bern (BE68/15), and Lucerne (LU04/14); these fish…
Understanding Kfamscan
Understanding Kfamscan 0 I am doing functional prediction of bacteria, to do that I have a list of selected KO that are involved in the target functionality for example nitrogen fixation, phosphorous solubilization etc. First I obtain the KOs of my bacterial proteomes and do search for the KOs involved…
KEGG COMPOUND: C00096
KEGG COMPOUND: C00096 COMPOUND: C00096 Help Entry C00096 Compound Name GDP-mannose;GDP-D-mannose;GDP-alpha-D-mannose Formula C16H25N5O16P2 Exact mass 605.0772 Mol weight 605.3411 Structure Mol fileKCF fileDB search Remark Reaction Pathway map00051 Fructose and mannose metabolism map00053 Ascorbate and aldarate metabolism map00520 Amino sugar and nucleotide sugar metabolism map00541 O-Antigen nucleotide sugar biosynthesis map00571 …
The evolutionary origin of host association in the Rickettsiales
Salje, J. Cells within cells: Rickettsiales and the obligate intracellular bacterial lifestyle. Nat. Rev. Microbiol. 19, 375–390 (2021). CAS PubMed Article Google Scholar Wang, S. & Luo, H. Dating Alphaproteobacteria evolution with eukaryotic fossils. Nat. Commun. 12, 3324 (2021). CAS PubMed PubMed Central Article Google Scholar Strassert, J. F. H.,…
Immune Infiltration and N(6)-Methyladenosine ncRNA Isoform Detection in Acute Lung Injury
Acute lung injury (ALI) is a severe form of sepsis that is associated with a high rate of morbidity and death in critically ill individuals. The emergence of ALI is the result of several factors at work. Case mortality rates might range from 40% to 70%. Researchers have discovered that…
UniProt: A0A6I9ZUN5_ACIJB
ID A0A6I9ZUN5_ACIJB Unreviewed; 234 AA. AC A0A6I9ZUN5; DT 07-OCT-2020, integrated into UniProtKB/TrEMBL. DT 07-OCT-2020, sequence version 1. DT 25-MAY-2022, entry version 6. DE SubName: Full=tumor necrosis factor ligand superfamily member 8 {ECO:0000313|RefSeq:XP_014931799.1}; GN Name=TNFSF8 {ECO:0000313|RefSeq:XP_014931799.1}; OS Acinonyx jubatus (Cheetah). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; OC Eutheria; Laurasiatheria;…
Table 2 | Bioinformatics Strategies for the Analysis of Lipids
Systems information PATHWAY Pathway maps (16 reference pathway maps, including a lipid structure map for unsaturated fatty acids; classified in “Lipid Metabolism”) 93,644 BRITE Functional hierarchies (“Lipid Metabolism” in pathway and KEGG Orthology classification, and “Lipids” classification based on LIPIDMAPS) 15,687 MODULE Pathway modules (80 modules are defined for pathways…
KEGG ENZYME: 1.14.19.32
Entry EC 1.14.19.32 Enzyme Name palmitoyl-CoA 14-(E/Z)-desaturase Class Oxidoreductases;Acting on paired donors, with incorporation or reduction of molecular oxygen;With oxidation of a pair of donors resulting in the reduction of O2 to two molecules of waterBRITE hierarchy Sysname palmitoyl-CoA,ferrocytochrome b5:oxygen oxidoreductase (14,15 cis/trans-dehydrogenating) Reaction(IUBMB) (1) palmitoyl-CoA + 2 ferrocytochrome b5 + O2…
KEGG ORTHOLOGY: K03191
KEGG ORTHOLOGY: K03191 ORTHOLOGY: K03191 Help Entry K03191 KO Symbol ureI Name acid-activated urea channel Pathway map05120 Epithelial cell signaling in Helicobacter pylori infection Brite KEGG Orthology (KO) [BR:ko00001] 09160 Human Diseases 09171 Infectious disease: bacterial 05120 Epithelial cell signaling in Helicobacter pylori infection K03191 ureI; acid-activated urea channel 09180 Brite Hierarchies 09183 Protein families: signaling and…
KEGG REACTION: R05288
Entry R05288 Reaction Name p-xylene, ferredoxin:oxygen oxidoreductase (methyl-hydroxylating) Definition p-Xylene + Oxygen + 2 Reduced ferredoxin + 2 H+ <=> 4-Methylbenzyl alcohol + 2 Oxidized ferredoxin + H2O Equation Reaction class Enzyme Pathway rn01120 Microbial metabolism in diverse environments rn01220 Degradation of aromatic compounds Module M00537 Xylene degradation, xylene => methylbenzoate…
KEGG COMPOUND: C07647
KEGG COMPOUND: C07647 COMPOUND: C07647 Help Entry C07647 Compound Name Phosphoramide mustard;Phosphamide mustard Formula C4H11Cl2N2O2P Exact mass 219.9935 Mol weight 221.0221 Structure Mol fileKCF fileDB search Reaction Pathway map00982 Drug metabolism – cytochrome P450 Other DBs KCF data Show ATOM 11 1 N1c N 23.8758 -15.8550 2 P1a P 23.8642 -17.2548 3 C1b C 22.6627 -15.1552 4 C1b C 25.0830 -15.1611 5 N1a N 25.2698 -17.2548 6 O1c O 23.8583 -18.6603 7 O3b O 22.4645 -17.2548 8 C1b C 21.4497 -15.8550 9 C1b C 26.2963 -15.8610 10 X Cl 20.2365 -15.1552 11 X Cl 27.5093 -15.1728BOND 10 1 1 2 1 2 1 3…
Pathway Enrichment
Pathway Enrichment 0 Is there any tool that can directly give me my gene id in first column and its pathway in second column? i am working with rice gene id. Thanks! KEGG ORA ENRICHMENT PATHWAY • 198 views • link updated 3 hours ago by newbio17 ▴ 350 •…
KEGG COMPOUND: C05172
Entry C05172 Compound Name Selenophosphoric acid;Selenophosphate Formula H3PO3Se Exact mass 161.8985 Mol weight 160.9558 Structure Mol fileKCF fileDB search Reaction Pathway Enzyme Other DBs KCF data Show ATOM 5 1 P1b P 25.0600 -18.6200 2 O1c O 23.6600 -18.6200 3 O1c O 26.4600 -18.6200 4 O1c O 25.0600 -20.0200 5 Z Se 25.0600 -17.2200BOND 4 1 1 2 1 2 1 3 1 3 1 4 2 4 1 5 1 Read more here: Source link
Table_8_RNA-Seq and 16S rRNA Analysis Revealed the Effect of Deltamethrin on Channel Catfish in the Early Stage of Acute Exposure.xls
Deltamethrin (Del) is a widely used pyrethroid insecticide and a dangerous material that has brought serious problems to the healthy breeding of aquatic animals. However, the toxicological mechanisms of Del on channel catfish remain unclear. In the present study, we exposed channel catfish to 0, 0.5, and 5 μg/L Del…
KEGG T01003: 286761
Entry 286761 CDS T01003 Symbol Vcpip1 Name (RefSeq) deubiquitinating protein VCPIP1 KO K11861 deubiquitinating protein VCIP135 [EC:3.4.19.12] Organism rno Rattus norvegicus (rat) Brite KEGG Orthology (KO) [BR:rno00001] 09180 Brite Hierarchies 09181 Protein families: metabolism 01002 Peptidases and inhibitors [BR:rno01002] 286761 (Vcpip1) 09182 Protein families: genetic information processing 04121 Ubiquitin system [BR:rno04121] 286761 (Vcpip1)Enzymes [BR:rno01000] 3. Hydrolases 3.4 Acting on peptide bonds (peptidases) 3.4.19 Omega peptidases 3.4.19.12 ubiquitinyl…
KEGG COMPOUND: C00311
KEGG COMPOUND: C00311 COMPOUND: C00311 Help Entry C00311 Compound Name Isocitrate;Isocitric acid;1-Hydroxytricarballylic acid;1-Hydroxypropane-1,2,3-tricarboxylic acid Formula C6H8O7 Exact mass 192.027 Mol weight 192.1235 Structure Mol fileKCF fileDB search Reaction Pathway map00630 Glyoxylate and dicarboxylate metabolism map00720 Carbon fixation pathways in prokaryotes map01060 Biosynthesis of plant secondary metabolites map01061 Biosynthesis of phenylpropanoids…
GitHub – ctlab/KEGG-network-pipeline
GitHub – ctlab/KEGG-network-pipeline This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository. You can’t perform that action at this time. You signed in with another tab or window. Reload to refresh your session. You signed out in another…
KEGG ENZYME: 3.2.1.104
KEGG ENZYME: 3.2.1.104 ENZYME: 3.2.1.104 Help Entry EC 3.2.1.104 Enzyme Name Class Hydrolases;Glycosylases;Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compoundsBRITE hierarchy Sysname cholesteryl-beta-D-glucoside glucohydrolase Reaction(IUBMB) cholesteryl-beta-D-glucoside + H2O = D-glucose + cholesterol [RN:R01460] Reaction(KEGG) Substrate Product Comment Acts on glucosides of cholesterol and sitosterol, but not on some related sterols…
KEGG COMPOUND: C00399
KEGG COMPOUND: C00399 COMPOUND: C00399 Help Entry C00399 Compound Name Ubiquinone;Coenzyme Q;CoQ;Q Formula C14H18O4(C5H8)n Structure Mol fileKCF fileDB search Comment Generic compound in reaction hierarchy n=5-9 Ubiquinone-6 [CPD:C17568] Ubiquinone-8 [CPD:C17569] Ubiquinone-9 [CPD:C01967] Ubiquinone-10 [CPD:C11378] [DR:D01065] Reaction Pathway Module M00142 NADH:ubiquinone oxidoreductase, mitochondria M00144 NADH:quinone oxidoreductase, prokaryotes M00145 NAD(P)H:quinone oxidoreductase, chloroplasts…
KEGG ORTHOLOGY: K06625
Brite KEGG Orthology (KO) [BR:ko00001] 09130 Environmental Information Processing 09132 Signal transduction 04012 ErbB signaling pathway K06625 CDKN1A, P21, CIP1; cyclin-dependent kinase inhibitor 1A 04630 JAK-STAT signaling pathway K06625 CDKN1A, P21, CIP1; cyclin-dependent kinase inhibitor 1A 04066 HIF-1 signaling pathway K06625 CDKN1A, P21, CIP1; cyclin-dependent kinase inhibitor 1A 04068 FoxO signaling pathway K06625 CDKN1A, P21, CIP1; cyclin-dependent kinase inhibitor 1A 04151 PI3K-Akt signaling pathway K06625 CDKN1A, P21,…
KEGG COMPOUND: C05924
KEGG COMPOUND: C05924 COMPOUND: C05924 Help Entry C05924 Compound Name Molybdopterin;Pyranopterin;H2Dtpp-mP Formula C10H14N5O6PS2 Exact mass 395.0123 Mol weight 395.3518 Structure Mol fileKCF fileDB search Reaction Pathway Module M00880 Molybdenum cofactor biosynthesis, GTP => molybdenum cofactor Enzyme Other DBs KCF data Show ATOM 24 1 S1a S 22.7500 -13.4003 2 S1a S 25.1308 -14.8087 3 C2y C 22.7383 -14.7666 4 C2y C 23.9353 -15.4866 5 C1y C 21.5555 -15.4809 6 C1y C 23.9236 -16.8776 7 C1y C 21.5496 -16.8718 8 N1x N 20.3269 -14.7608 9 C1b…
MND1 Expression as a Predictor of Breast Cancer Survival
Introduction Breast cancer (BC) is the most commonly diagnosed cancer in women, and it is the main cause of cancer mortality in women around the world.1 Although standard treatments for breast cancer, including surgery, radiotherapy, chemotherapy, endocrine therapy, targeted therapy, and immunotherapy, have greatly improved during the last few decades.2,3…
Role of CD68 in tumor immunity and prognosis prediction in pan-cancer
Expression of CD68 in pan-cancer First, to fully clarify the expression of CD68 in pan-cancer, we matched the GTEx normal samples with TCGA tumor samples (Fig. 1A). We found that the levels of CD68 were significantly elevated (P < 0.01) in colon adenocarcinoma (COAD), glioblastoma multiforme (GBM), kidney renal clear cell carcinoma (KIRC),…
Circulating cell-free mtDNA release is associated with the activation of cGAS-STING pathway and inflammation in mitochondrial diseases
Craven L, Alston C, Taylor R, Turnbull D (2017) Recent advances in mitochondrial disease. Annu Rev Genomics Hum Genet 18:257–275. doi.org/10.1146/annurev-genom-091416-035426 CAS Article PubMed Google Scholar El-Hattab AW, Adesina AM, Jones J, Scaglia F (2015) MELAS syndrome: clinical manifestations, pathogenesis, and treatment options. Mol Genet Metab 116(1–2):4–12. doi.org/10.1016/j.ymgme.2015.06.004 CAS Article …
Differential Expression Profiles and Bioinformatics Analysis of tRNA-Derived Small RNAs in Muscle-Invasive Bladder Cancer in a Chinese Population
This article was originally published here Genes (Basel). 2022 Mar 28;13(4):601. doi: 10.3390/genes13040601. ABSTRACT Muscle-invasive bladder cancer (MIBC) leads to a large societal burden. Recently, tRNA-derived small RNAs (tsRNAs), a novel type of noncoding RNA (ncRNAs), have been identified. However, the expression patterns and functions of tsRNAs in MIBC have…
KEGG COMPOUND: C05345
KEGG COMPOUND: C05345 COMPOUND: C05345 Help Entry C05345 Compound Name beta-D-Fructose 6-phosphate;beta-D-Fructofuranose 6-phosphate Formula C6H13O9P Exact mass 260.0297 Mol weight 260.1358 Structure Mol fileKCF fileDB search Reaction Pathway map00010 Glycolysis / Gluconeogenesis map00051 Fructose and mannose metabolism map00520 Amino sugar and nucleotide sugar metabolism map00541 O-Antigen nucleotide sugar biosynthesis map00997 …
Construction of a circRNA-Mediated ceRNA Network Reveals Novel Biomarkers for Aortic Dissection
Background: Aortic dissection (AD) is a rare and lethal disorder with its genetic basis remains largely unknown. Many studies have confirmed that circRNAs play important roles in various physiological and pathological processes. However, the roles of circRNAs in AD are still unclear and need further investigation. The present study aimed…
KEGG MODULE: M00567
MODULE: M00567 Help Entry M00567 Pathway Module Name Methanogenesis, CO2 => methane Definition (K00200+K00201+K00202+K00203-K11261+(K00205,K11260,K00204)) K00672 K01499 (K00319,K13942) K00320 (K00577+K00578+K00579+K00580+K00581-K00582-K00583+K00584) (K00399+K00401+K00402) (K22480+K22481+K22482,K03388+K03389+K03390,K08264+K08265,K03388+K03389+K03390+K14127+(K14126+K14128,K22516+K00125)) Diagram Orthology 4Fe-4S ferredoxin formylmethanofuran–tetrahydromethanopterin N-formyltransferase [EC:2.3.1.101] [RN:R03390] methenyltetrahydromethanopterin cyclohydrolase [EC:3.5.4.27] [RN:R03464] methylenetetrahydromethanopterin dehydrogenase [EC:1.5.99.9] [RN:R04456] 5,10-methenyltetrahydromethanopterin hydrogenase [EC:1.12.98.2] [RN:R04455] coenzyme F420-dependent N5,N10-methenyltetrahydromethanopterin reductase [EC:1.5.99.11] [RN:R04464] Ortholog tableTaxonomyModule table…
N6-methyladenosine modification of CENPK mRNA by ZC3H13 promotes cervical cancer stemness and chemoresistance | Military Medical Research
Bioinformatics analyses revealed the involvement of m6A modification in cervical cancer progression To better understand whether and how m6A regulators contribute to cervical cancer progression, we first identified 9 m6A writers (WTAP, ZC3H13, METTL3, METTL14, METTL16, VIRMA, RBM15B, RBM15, and CBLL1), 15 m6A readers (FMR1, hnRNPA2B1, hnRNPC, YTHDF1/2/3, YTHDC1/2, LRPPRC,…
A hypoxia-related signature in lung squamous cell carcinoma
Introduction Lung cancer is the major leading cause of tumour-related deaths throughout the world, while lung squamous cell carcinoma (LUSC) as the second most common histological type of lung cancer.1 Each year, almost 1.8 million people are diagnosed with lung cancer worldwide and 400,000 of these die from LUSC.2,3 Due to…
Bioconductor – keggorthology
This package is for version 2.13 of Bioconductor; for the stable, up-to-date release version, see keggorthology. graph support for KO, KEGG Orthology Bioconductor version: 2.13 graphical representation of the Feb 2010 KEGG Orthology. The KEGG orthology is a set of pathway IDs that are not to be confused…
Bioconductor – neaGUI
This package is for version 2.13 of Bioconductor; for the stable, up-to-date release version, see neaGUI. An R package to perform the network enrichment analysis (NEA). Bioconductor version: 2.13 neaGUI is an easy to use R package developed to perform the network enrichment analysis (NEA) proposed by Alexeyenko…
Bioinformatics analysis identifies widely expressed genes
1Department of Orthopedics, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, People’s Republic of China; 2Department of Pediatrics, The Shanxi Medical University, Taiyuan, Shanxi, People’s Republic of China Correspondence: Jun Qian, Department of Orthopedics, The First Affiliated Hospital of Anhui Medical University, 218 Jixi Road, Hefei, 230022, Anhui,…
A multi-omics approach to elucidate the mechanisms of action of a dietary muramidase administered to broiler chickens
Gadde, U., Kim, W. H., Oh, S. T. & Lillehoj, H. S. Alternatives to antibiotics for maximizing growth performance and feed efficiency in poultry: a review. Animal Health Res. Rev. 18, 26–45 (2017). CAS Google Scholar Smits, C. H. M., Li, D., Patience, J. F. & den Hartog, L. A….
Metagenomic data-analysis reveals enrichment of lipopolysaccharide synthesis in the gut microbiota of atrial fibrillation patients
This article was originally published here Zhonghua Xin Xue Guan Bing Za Zhi. 2022 Mar 24;50(3):249-256. doi: 10.3760/cma.j.cn112148-20210106-00015. ABSTRACT Objective: To investigate the functional changes of key gut microbiota (GM) that produce lipopolysaccharide (LPS) in atrial fibrillation (AF) patients and to explore their potential role in the pathogenesis of AF….
KEGG COMPOUND: C01380
Entry C01380 Compound Name Ethylene glycol;1,2-Ethanediol;Ethane-1,2-diol Formula C2H6O2 Exact mass 62.0368 Mol weight 62.0678 Structure Mol fileKCF fileDB search Reaction Pathway map00625 Chloroalkane and chloroalkene degradation map00630 Glyoxylate and dicarboxylate metabolism map01120 Microbial metabolism in diverse environments Enzyme Other DBs KCF data Show ATOM 4 1 C1b C 28.1392 -16.3327 2 C1b C 29.5408 -16.3327 3 O1a O 27.4444 -17.5473 4 O1a O 30.2356 -17.5473BOND 3 1 1 2 1 2 1 3 1 3 2 4 1…
Identification of potentially functional circular RNAs hsa_circ_0070934 and hsa_circ_0004315 as prognostic factors of hepatocellular carcinoma by integrated bioinformatics analysis
Rawla, P., Sunkara, T., Muralidharan, P. & Raj, J. P. Update in global trends and aetiology of hepatocellular carcinoma. Contemp. Oncol. (Poznan, Poland) 22, 141–150 (2018). CAS Google Scholar Kong, D. et al. Current statuses of molecular targeted and immune checkpoint therapies in hepatocellular carcinoma. Am. J. Cancer Res. 10,…
KEGG REACTION: R01627
KEGG REACTION: R01627 REACTION: R01627 Help Entry R01627 Reaction Name 3-dehydroshikimate hydro-lyase Definition 3-Dehydroshikimate <=> 3,4-Dihydroxybenzoate + H2O Equation Reaction class Enzyme Pathway rn01053 Biosynthesis of siderophore group nonribosomal peptides rn01110 Biosynthesis of secondary metabolites Orthology Other DBs LinkDB All DBs DBGET integrated database retrieval system Read more here: Source…
KEGG COMPOUND: C02538
KEGG COMPOUND: C02538 COMPOUND: C02538 Help Entry C02538 Compound Name Formula C18H22O5S Exact mass 350.1188 Mol weight 350.4293 Structure Mol fileKCF fileDB search Reaction Pathway map00140 Steroid hormone biosynthesis Enzyme Brite Compounds with biological roles [BR:br08001] Hormones and transmitters Steroid hormones Estrogens C02538 Estrone 3-sulfateLipids [BR:br08002] ST Sterol lipids ST02 Steroids ST0201 C18 steroids (estrogens) and derivatives C02538 Estrone 3-sulfate ST05 Steroid…
Frontiers | Machine Learning and Deep Learning Applications in Metagenomic Taxonomy and Functional Annotation
Introduction The study of the microbial environments has benefited from the sequencing revolution, where technology improvement decreased the DNA sequencing cost and increased the number of sequenced nucleic bases. For approximately 20 years (depending on how we define the term metagenomics), it has allowed the decryption of the microbial composition…
Function of SYDE C2-RhoGAP family as signaling hubs for neuronal development deduced by computational analysis
Hallam, S. J., Goncharov, A., McEwen, J., Baran, R. & Jin, Y. Syd-1, a presynaptic protein with PDZ, C2 and rhoGAP-like domains specifies axon identity in C. elegans. Nat. Neurosci. 5, 1137–1146 (2002). CAS PubMed Google Scholar Xu, Y. & Quinn, C. C. SYD-1 promotes multiple developmental steps leading to…
KEGG ORTHOLOGY: K13942
KEGG ORTHOLOGY: K13942 ORTHOLOGY: K13942 Help Entry K13942 KO Symbol hmd Name 5,10-methenyltetrahydromethanopterin hydrogenase [EC:1.12.98.2] Pathway map01120 Microbial metabolism in diverse environments Module M00567 Methanogenesis, CO2 => methane Brite KEGG Orthology (KO) [BR:ko00001] 09100 Metabolism 09102 Energy metabolism 00680 Methane metabolism K13942 hmd; 5,10-methenyltetrahydromethanopterin hydrogenaseEnzymes [BR:ko01000] 1. Oxidoreductases 1.12 Acting on hydrogen as donor 1.12.98 With other, known, physiological acceptors 1.12.98.2 5,10-methenyltetrahydromethanopterin…
Efficient way of mapping UniProt IDs to representative UniRef90 IDs?
You can do this directly on UniProt: www.uniprot.org/uploadlists/ Just paste or upload your list of UniProt IDs, and select “UniProtKB AC/ID” in the “From” field and “UniParc” in the “To” field I’ve also written a script, pasted below, that can do this with some useful options: $ uniprot_map.pl -h uniprot_map.pl…
Identification of Hub Genes Associated with COPD Through Integrated Bi
Introduction Chronic obstructive pulmonary disease (COPD) will become the third leading cause of death worldwide.1,2 The incidence of COPD worldwide is 13.1%3 and is 13.7% in the Chinese population over 40 years of age.4 Emphysema is one of the most common phenotypes.1 Over the past few decades, we have conducted…
KEGG COMPOUND: C01113
KEGG COMPOUND: C01113 COMPOUND: C01113 Help Entry C01113 Compound Name D-Galactose 6-phosphate;6-Phospho-D-galactose Formula C6H13O9P Exact mass 260.0297 Mol weight 260.1358 Structure Mol fileKCF fileDB search Reaction Pathway map02060 Phosphotransferase system (PTS) Enzyme Other DBs KCF data Show ATOM 16 1 P1b P 25.9015 -16.0011 2 O2b O 27.3009 -16.0070 3 O1c O 25.8898 -17.4005 4 O1c O 24.5021 -16.0011 5 O1c O 25.8898 -14.6076 6 C1b C 28.3679 -15.0973 7 C1y C 29.5748 -15.8029 8 C1y C 29.5748 -17.2021 9 O2x O 30.7818 -15.0973 10 C1y C 30.7818 -17.9018 11 O1a O 28.3679 -17.9018 12 C1y C 32.0005 -15.8029 13 C1y…
KEGG COMPOUND: C00469
KEGG COMPOUND: C00469 COMPOUND: C00469 Help Entry C00469 Compound Name Ethanol;Ethyl alcohol;Methylcarbinol Formula C2H6O Exact mass 46.0419 Mol weight 46.0684 Structure Mol fileKCF fileDB search Remark Reaction Pathway map00010 Glycolysis / Gluconeogenesis map01110 Biosynthesis of secondary metabolites map01120 Microbial metabolism in diverse environments map04750 Inflammatory mediator regulation of TRP channels…